I'm writing a paper comparing the performance of 2 algorithms (lets call them A and B). A performs better than B, however preliminary data suggested a way to significantly improve the performance of B. I made the changes to B and sure enough now B outperforms A. I've verified that it's not just a fluke of the specific inputs I was testing against, making the changes to B leads to consistently better performance.
What is the best way to write these findings up? It feels an awful lot like cherry picking to me (especially since I didn't know when I started that I could improve B and for all I know there are improvements to A that could make it better than the improved B)
But despite its questionable origins the modified algorithm does perform the task faster and I want to include that information in my paper.
What is the best approach to take? Call the modified version Algorithm C and just add it to the paper? Add this information to the appendix? Something else?